Spinal nerve transection (SNT) of the L5 spinal nerve was performed. Dorsal root ganglia (DRG) were harvested 7 days after surgery fresh dissection
Extracted molecule
polyA RNA
Extraction protocol
RNA extracted using the miRNEasy kit (QIAGEN) according to manufacturer’s instructions. RNA concentration was measured using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA).
Label
biotin
Label protocol
Standard protcol performed by UCL genomics, following Affymetrix instructions
Hybridization protocol
Standard protcol performed by UCL genomics, following Affymetrix instructions
Scan protocol
Standard protcol performed by UCL genomics, following Affymetrix instructions
Data processing
CEL files were processed in R using the oligo Bioconductor package. Background correction, normalisation and summarisation were performed using robust multi-array average (RMA), quantile normalisation and median polish respectively. Summarisation was performed at the exon level (where each probeset corresponds to an exon, with some exons being probed by more than one probeset) or the transcript cluster/gene level, where all probesets from different exons belonging to the same gene were summarised to produce a single transcript cluster measurement.
Whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat, at different sequencing depths (Affymetrix exon-level)
